I figured I would share what I posted recently to one of my old friends who has recently developed an autoimmune issue:
I developed some kind of autoimmune issue seven years ago. It got to the point I couldn't get out of bed due to widespread body pain and debilitating fatigue. I felt like I had the flu and was hit by a truck on the same day. A game changer for me was cutting out gluten, dairy, soy, corn, and nightshades. I always eat that way now. I went paleo for a while and it was great. But, then I got lazy and quit. I'm actually starting back up with paleo/keto within the next few weeks. ... I'm weaning myself off of sugar right now. It sucks. I also have to avoid artificial anything or it can cause a flair: dye, preservative, flavors, etc. I've become an expert at reading labels. You quickly learn which brands are safe and it becomes a lot less overwhelming.
Tips: understand you are going to be changing the way you eat. Do not try to recreate the standard American diet but using paleo ingredients. I personally think that is where people fail. Sure, I'll bake an occasional cake or cookie, but for the most part I rarely use my gluten free flours and I never but gluten free bread. I eat foods that look like they do coming from nature.
The first month was the hardest for me. I mourned the loss of what I couldn't do anymore. But now seven years in, I don't even miss that stuff. I actually had an Oreo the other day as a cheat. It tasted gross to me (and I loved oreos).
You can do this!
I don't know how you are doing about energy and muscle pain, but the one supplement that was miraculous for me in that regard was d-ribose. It is a sugar your body is supposed to make for energy in removing lactic acid and functioning. I'm guessing my muscle pain was built up lactic acid because the ribose made it go away. Life saver, literally!
I've got lots of other suggestions, but starting with diet will give you the biggest changes. You can tweak with supplements after that.
Bring a notebook while shopping to write down brands that are diet approved.